Contacts of the strand formed by residues 97 - 108 (chain D) in PDB entry 1UHG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 97 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C GLN* 4.1 3.2 + - - +
89D GLN* 3.6 11.6 + - - +
90D ILE* 3.4 41.1 - - + +
94D ASN* 2.9 51.0 + - - +
95D ASP 3.9 0.4 - - - -
96D VAL* 1.3 95.9 - - + +
98D SER* 1.3 75.2 + - - +
99D PHE* 4.4 1.6 - - + -
180D PHE* 4.0 17.9 - + + -
181D LYS 3.3 14.4 - - - +
182D GLY* 3.6 9.4 - - - -
234D PHE* 5.9 4.7 - - + -
235D ALA 4.7 5.4 - - - -
238D THR* 4.0 21.0 + - + +
239D MET* 3.9 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C SER 4.4 6.8 + - - -
152C GLN* 4.3 21.5 + - - -
154C ASN* 4.4 19.5 + - - -
97D TYR* 1.3 79.0 + - - +
99D PHE* 1.3 61.8 + - - +
100D SER* 4.2 4.9 - - - -
179D VAL 3.7 0.8 - - - +
180D PHE* 3.3 6.8 - - - -
181D LYS* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D CYS* 4.5 10.3 - - - -
32D ILE* 4.7 2.5 - - + -
33D ALA* 5.2 0.4 - - + -
87D LEU* 4.5 8.1 - - + -
90D ILE* 3.4 48.0 + - + +
91D THR* 3.7 39.1 - - + +
97D TYR* 4.4 6.1 - - + -
98D SER* 1.3 75.3 - - - +
100D SER* 1.3 60.8 + - - +
101D LEU* 4.0 20.3 + - + -
178D ILE* 4.2 18.4 - - + -
179D VAL 3.4 5.8 - - - -
180D PHE* 4.2 12.8 - + + -
239D MET* 5.5 2.0 - - + -
377D LEU* 5.6 0.9 - - + -
378D PHE* 3.6 38.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ASN* 4.8 3.6 + - - -
98D SER* 5.2 4.3 - - - -
99D PHE* 1.3 75.7 + - - +
101D LEU* 1.3 60.8 + - - +
152D GLN 4.1 18.6 + - - -
153D THR* 4.8 6.7 - - - +
154D ASN* 4.0 12.9 + - - -
177D ALA 3.7 0.7 - - - +
178D ILE* 3.1 7.1 - - - +
179D VAL* 2.8 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ALA* 3.8 15.5 - - + -
36D SER* 5.2 6.5 - - - +
87D LEU* 3.9 30.1 - - + -
91D THR* 4.5 13.6 - - + +
99D PHE* 4.0 15.5 + - + -
100D SER* 1.3 74.3 - - - +
102D ALA* 1.3 60.3 + - - +
103D SER* 4.0 25.6 + - - +
148D TRP* 5.4 0.2 - - - -
152D GLN* 4.5 12.9 + - - -
176D ASN* 4.1 3.6 - - - +
177D ALA 3.5 4.3 - - - +
178D ILE* 3.1 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D SER 4.2 0.2 - - - -
101D LEU* 1.3 72.1 - - - +
103D SER* 1.3 58.6 + - - +
148D TRP* 3.8 26.6 - - + -
149D VAL* 4.4 7.8 - - + +
152D GLN* 4.0 23.6 - - + -
153D THR* 4.3 12.8 - - + -
175D VAL* 3.5 6.4 - - - +
177D ALA* 2.8 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ALA 4.8 0.2 + - - -
36D SER* 5.2 2.3 + - - -
37D ALA* 3.7 18.9 + - - +
40D MET* 4.2 13.6 - - - +
101D LEU* 3.8 19.1 + - - +
102D ALA* 1.3 74.7 - - - +
104D ARG* 1.3 66.0 + - - +
127D GLY 4.4 1.6 - - - +
128D GLY* 4.1 11.8 - - - -
148D TRP* 3.7 5.7 - - - -
174D LEU* 4.9 0.9 - - - +
175D VAL 3.2 4.3 + - - -
176D ASN* 3.1 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ASP* 2.8 37.4 + - - +
339C ARG* 6.2 2.0 - - - +
40D MET* 5.3 2.2 - - - -
103D SER* 1.3 79.4 + - - +
105D LEU* 1.3 71.8 + - - +
106D TYR* 3.2 46.4 + - + -
127D GLY 2.8 19.5 + - - +
128D GLY* 3.3 14.1 - - - +
129D LEU 4.6 0.4 - - - +
130D GLU* 3.4 27.1 + - - +
148D TRP* 3.3 41.1 - - + +
173D VAL 3.6 1.2 - - - +
174D LEU* 3.6 5.7 - - - +
175D VAL* 2.9 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D MET* 4.8 11.2 - - + -
41D VAL* 3.8 29.4 - - + +
104D ARG* 1.3 75.6 - - - +
106D TYR* 1.3 57.9 + - - +
107D ALA 4.0 0.2 - - - -
117D TYR* 3.9 20.4 - - - +
128D GLY 2.6 13.7 + - - +
129D LEU* 3.3 18.5 - - + +
130D GLU 2.9 24.8 + - - -
172D MET* 3.8 36.6 - - + -
173D VAL 3.4 1.3 - - - +
174D LEU* 3.8 35.0 - - + -
315D ILE* 4.8 2.0 - - + -
323D ILE* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ARG* 3.2 47.7 + - + -
105D LEU* 1.3 72.2 - - - +
107D ALA* 1.3 60.4 + - - +
130D GLU* 3.2 23.6 - - + +
131D PRO 5.1 0.9 - - - -
132D ILE* 4.1 20.2 - - + -
134D PHE* 3.6 11.0 - - + -
144D LEU* 4.6 2.7 + - + -
145D ILE* 3.7 53.5 - - + -
148D TRP* 3.4 23.0 - + - +
172D MET* 3.2 4.7 - - - +
173D VAL* 2.9 41.9 + - + +
175D VAL* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU 3.9 1.0 + - - -
106D TYR* 1.3 74.8 - - - +
108D GLU* 1.3 70.7 + - - +
109D GLU 3.1 0.2 + - - -
111D TYR* 4.9 6.5 - - + -
113D ILE* 4.6 15.0 - - + -
129D LEU* 4.3 13.2 - - + -
130D GLU 2.9 8.4 + - - +
131D PRO* 3.2 6.5 - - + +
132D ILE 2.9 21.3 + - - -
134D PHE* 4.2 2.2 - - - -
171D ALA 3.7 5.2 - - - +
172D MET* 3.8 21.8 - - + -
321D LEU* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ALA* 1.3 72.5 - - - +
109D GLU* 1.3 74.0 + - - +
110D ARG* 2.9 47.0 + - + +
111D TYR* 3.0 44.8 + - + +
131D PRO* 5.2 0.3 - - - +
132D ILE 3.3 8.5 - - - +
133D ASN* 3.4 7.4 - - - +
134D PHE* 2.8 35.7 + - + -
135D GLN* 3.0 26.4 + - + +
170D THR 3.8 16.8 - - - +
171D ALA 2.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il